LOCUS       NM_001378633            1456 bp    mRNA    linear   PRI 01-JUN-2024
DEFINITION  Homo sapiens visual system homeobox 1 (VSX1), transcript variant
            10, mRNA.
ACCESSION   NM_001378633
VERSION     NM_001378633.1
KEYWORDS    RefSeq.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 1456)
  AUTHORS   Deva,J.P., Ngeow,Y.F. and Zin,T.
  TITLE     The association between VSX1 exon3 gene variants and keratoconus in
            Malaysian patients
  JOURNAL   Indian J Ophthalmol 71 (6), 2443-2447 (2023)
   PUBMED   37322657
  REMARK    GeneRIF: The association between VSX1 exon3 gene variants and
            keratoconus in Malaysian patients.
REFERENCE   2  (bases 1 to 1456)
  AUTHORS   Ma,W., Li,X., Yang,L., Pan,J., Chen,Y., Lu,Y., Dong,X., Li,D. and
            Gan,W.
  TITLE     High VSX1 expression promotes the aggressiveness of clear cell
            renal cell carcinoma by transcriptionally regulating FKBP10
  JOURNAL   J Transl Med 20 (1), 554 (2022)
   PUBMED   36463181
  REMARK    GeneRIF: High VSX1 expression promotes the aggressiveness of clear
            cell renal cell carcinoma by transcriptionally regulating FKBP10.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1456)
  AUTHORS   Haenig,C., Atias,N., Taylor,A.K., Mazza,A., Schaefer,M.H., Russ,J.,
            Riechers,S.P., Jain,S., Coughlin,M., Fontaine,J.F., Freibaum,B.D.,
            Brusendorf,L., Zenkner,M., Porras,P., Stroedicke,M., Schnoegl,S.,
            Arnsburg,K., Boeddrich,A., Pigazzini,L., Heutink,P., Taylor,J.P.,
            Kirstein,J., Andrade-Navarro,M.A., Sharan,R. and Wanker,E.E.
  TITLE     Interactome Mapping Provides a Network of Neurodegenerative Disease
            Proteins and Uncovers Widespread Protein Aggregation in Affected
            Brains
  JOURNAL   Cell Rep 32 (7), 108050 (2020)
   PUBMED   32814053
REFERENCE   4  (bases 1 to 1456)
  AUTHORS   Kalasidou,G., Frydas,I., Kozei,A., Syrmakesi,P., Loukovitis,E.,
            Sfakianakis,K., Balidis,M., Zachariadis,Z., Tranos,P., Kozeis,N.
            and Anogeianakis,G.
  TITLE     Contributions of VSX1 gene to keratoconus
  JOURNAL   J Biol Regul Homeost Agents 32 (6), 1515-1518 (2018)
   PUBMED   30574758
  REMARK    GeneRIF: VSX1 is involved in keratoconus and other corneal
            pathologies
REFERENCE   5  (bases 1 to 1456)
  AUTHORS   Dorval,K.M., Bobechko,B.P., Ahmad,K.F. and Bremner,R.
  TITLE     Transcriptional activity of the paired-like homeodomain proteins
            CHX10 and VSX1
  JOURNAL   J Biol Chem 280 (11), 10100-10108 (2005)
   PUBMED   15647262
  REMARK    GeneRIF: CHX10 and VSX1 may control retinal bipolar cell
            specification or differentiation by repressing genes required for
            the development of other cell types
REFERENCE   6  (bases 1 to 1456)
  AUTHORS   Bisceglia,L., Ciaschetti,M., De Bonis,P., Campo,P.A., Pizzicoli,C.,
            Scala,C., Grifa,M., Ciavarella,P., Delle Noci,N., Vaira,F.,
            Macaluso,C. and Zelante,L.
  TITLE     VSX1 mutational analysis in a series of Italian patients affected
            by keratoconus: detection of a novel mutation
  JOURNAL   Invest Ophthalmol Vis Sci 46 (1), 39-45 (2005)
   PUBMED   15623752
  REMARK    GeneRIF: Mutational analysis of the VSX1 gene in a series of
            Italian patients revealed one novel mutation and confirmed an
            important role played by this gene in a significant proportion of
            patients affected by keratoconus
            GeneRIF: Observational study of genotype prevalence. (HuGE
            Navigator)
REFERENCE   7  (bases 1 to 1456)
  AUTHORS   Mintz-Hittner,H.A., Semina,E.V., Frishman,L.J., Prager,T.C. and
            Murray,J.C.
  TITLE     VSX1 (RINX) mutation with craniofacial anomalies, empty sella,
            corneal endothelial changes, and abnormal retinal and auditory
            bipolar cells
  JOURNAL   Ophthalmology 111 (4), 828-836 (2004)
   PUBMED   15051220
  REMARK    GeneRIF: The new mutation in the VSX1 (RINX) gene described in this
            report results in abnormal craniofacial features, absence of the
            roof of the sella turcica, and anomalous development of the corneal
            endothelium.
REFERENCE   8  (bases 1 to 1456)
  AUTHORS   Heon,E., Greenberg,A., Kopp,K.K., Rootman,D., Vincent,A.L.,
            Billingsley,G., Priston,M., Dorval,K.M., Chow,R.L., McInnes,R.R.,
            Heathcote,G., Westall,C., Sutphin,J.E., Semina,E., Bremner,R. and
            Stone,E.M.
  TITLE     VSX1: a gene for posterior polymorphous dystrophy and keratoconus
  JOURNAL   Hum Mol Genet 11 (9), 1029-1036 (2002)
   PUBMED   11978762
  REMARK    GeneRIF: Mutations in VSX1 homeobox gene results in impaired DNA
            binding and is associated with posterior polymorphous dystrophy and
            keratoconus
REFERENCE   9  (bases 1 to 1456)
  AUTHORS   Hayashi,T., Huang,J. and Deeb,S.S.
  TITLE     RINX(VSX1), a novel homeobox gene expressed in the inner nuclear
            layer of the adult retina
  JOURNAL   Genomics 67 (2), 128-139 (2000)
   PUBMED   10903837
REFERENCE   10 (bases 1 to 1456)
  AUTHORS   Semina,E.V., Mintz-Hittner,H.A. and Murray,J.C.
  TITLE     Isolation and characterization of a novel human paired-like
            homeodomain-containing transcription factor gene, VSX1, expressed
            in ocular tissues
  JOURNAL   Genomics 63 (2), 289-293 (2000)
   PUBMED   10673340
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL080312.14.
            
            Summary: The protein encoded by this gene contains a paired-like
            homeodomain and binds to the core of the locus control region of
            the red/green visual pigment gene cluster. The encoded protein may
            regulate expression of the cone opsin genes early in development.
            Mutations in this gene can cause posterior polymorphous corneal
            dystrophy and keratoconus. Alternatively spliced transcript
            variants encoding different isoforms have been described. [provided
            by RefSeq, Jul 2008].
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1803615.90241.1,
                                           SRR1803612.19749.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968968, SAMEA2145743
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-368               AL080312.14        50014-50381         c
            369-1456            AL080312.14        47792-48879         c
FEATURES             Location/Qualifiers
     source          1..1456
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="20"
                     /map="20p11.21"
     gene            1..1456
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPCD1; PPD;
                     RINX"
                     /note="visual system homeobox 1"
                     /db_xref="GeneID:30813"
                     /db_xref="HGNC:HGNC:12723"
                     /db_xref="MIM:605020"
     exon            1..368
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPCD1; PPD;
                     RINX"
                     /inference="alignment:Splign:2.1.0"
     CDS             254..658
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPCD1; PPD;
                     RINX"
                     /note="isoform e is encoded by transcript variant 10;
                     transcription factor VSX1; retinal inner nuclear layer
                     homeobox protein; homeodomain protein RINX; visual system
                     homeobox 1 homolog, CHX10-like"
                     /codon_start=1
                     /product="visual system homeobox 1 isoform e"
                     /protein_id="NP_001365562.1"
                     /db_xref="GeneID:30813"
                     /db_xref="HGNC:HGNC:12723"
                     /db_xref="MIM:605020"
                     /translation="MAEYGLYGAMVRHCIPLPDSVLNSAEGGLLGSCAPWLLGMHKKS
                     MGMIRKPGSEDKLAGLWGSDHFKEGSSQSESGSQRGSDKVSPENGLEDVAIDLSSSAR
                     QETKKVHPGAGAQGGSNSTALEGPQPGKVGAT"
     exon            369..1456
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPCD1; PPD;
                     RINX"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1433..1438
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPCD1; PPD;
                     RINX"
                     /note="hexamer: AATAAA"
     polyA_site      1456
                     /gene="VSX1"
                     /gene_synonym="CAASDS; KTCN; KTCN1; PPCD; PPCD1; PPD;
                     RINX"
                     /note="major polyA site"
ORIGIN      
        1 gctgggggct cctgggcgct ctccctgagg gcggctggtt ggccctcggg agctatttcc
       61 ttcagaaata gcatgggatc atgctcggga gagaagatcc gagccctggg acgccgcctc
      121 cgctcctcca ggcgcccctc ttcactgtct cttctgtgtg ccttctgctt ctcctgcctc
      181 caaccaggtc tggtttcaaa accgcagggc caaatggcgc aagcgggaga agcgctgggg
      241 cggcagcagc gtgatggccg agtacgggct gtacggggcc atggtgcgcc actgcatccc
      301 gctgccagac tccgtgctca actccgccga gggcggcctg ctgggctcct gcgcgccctg
      361 gctcctgggg atgcataaaa aatccatggg gatgataagg aagccaggaa gtgaagataa
      421 gttggcagga ctctggggct ctgaccactt caaagaaggt tctagccaga gtgagtcagg
      481 atcacagaga ggctcagata aagtgagccc tgagaatggc ttggaagatg tggctattga
      541 cctctccagc tctgcccggc aggagaccaa gaaagtgcac cctggggctg gtgctcaagg
      601 aggctccaac tccacggcac tggaggggcc ccagccaggg aaggtgggag ccacatgaga
      661 cccacaggtc ccactgtcaa aggctgaaaa tgtgcatatt cctcactggc attttccaaa
      721 agacaaaaat tgtccaagac atatactctc agtttgattt tcttctgaca atgtcaagat
      781 aaaatgcaat gccacttgct ttaagaggac agatgagtga cctagggaaa attctatttc
      841 attctagaat ggaaacggtt ccttaatggc actttaacca gttaacttgg tgcaaaactt
      901 ttgattctct tttgtagctt gagcagggag gatccgaagt tcaaaaatga tttcactgct
      961 gggcatcatt tgagatgtgt ggttcaatgt actgtataga tgaataggtt aggtctgatg
     1021 tcctcattct caattaggaa atataaaatt gtttaatatc cagaagaatc tgatatcatc
     1081 atagtgaaga ctccatacag acacatgaat gaattatatt gtctttacct tgaacttggc
     1141 cttggatatt tcaattttct tgttagggag taattttgtg ttttcttgag tgtcacttga
     1201 taggctatgc atattggaat tcaaagaaac ccatactcta gtcgtttctg catttccttt
     1261 aaaaatagca tgggatcata tttaaacaat tgttggatag ctggaaacag tgtttttagg
     1321 tcagaccagg cttttggtct ttcaaaattt gtgattgaaa gcactttagt gacttggatt
     1381 ttgtaaatct ttcctttcct gcgtttcctt tgccatttat ttattcttta aaaataaaca
     1441 ttttgtggtg tgttta
//
